Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK

  • Heidelberg

 

Educators:
Axel von Kamp, Steffen Klamt, Sven Thiele (MPI Magdeburg), Frank T. Bergmann, Ursula Kummer (University of Heidelberg), Wolfgang Müller, Maja Rey, Andreas Weidemann, Ulrike Wittig (HITS) (de.NBI-SysBio)

Date:
Monday 18.03.2019 – Wednesday 20.03.2019

Location:
BioQuant
Im Neuenheimer Feld 267
Ruprecht-Karls-Universität Heidelberg
69120 Heidelberg

Contents:
Key concepts of stoichiometric and kinetic modeling of biochemical networks:
- stoichiometric matrix and stoichiometric networks
- steady state flux distributions
- principles of constraint-based modeling
- metabolic flux analysis and flux optimization (flux balance analysis)
- metabolic pathway analysis with elementary flux modes
- metabolic network design via minimal cut sets
- simulation of dynamic (kinetic) models
- sensitivity analysis
- carrying out parameter estimation tasks
- model exchange using SBML
Data and model management:
- manual/programmatic access to reaction kinetics data from SABIO-RK
- storage and exchange of data and models using FAIRDOMHub/SEEK
- modeling specific functionalities in FAIRDOMHub/SEEK
 
Learning goals:
During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists.

The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks.

Prerequisites:
Some knowledge of mathematical modeling will be advantageous.
The participants should bring their own laptop with MATLAB installed (if you do not have MATLAB please let us know during registration).
Download and preinstallation of COPASI and CellNetAnalyzer is recommended but not mandatory.

Keywords:
CellNetAnalyzer (CNA), COPASI, SBML, FAIR, modeling, kinetic data access, database, data and model management

Tools:
CellNetAnalyzer, COPASI, Matlab, SABIO-RK, FAIRDOMHub/SEEK

Contact:
Frank T. Bergmann (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Sven Thiele  (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Ulrike Wittig (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Registration:
https://goo.gl/forms/6UNvjb7Amf0aZGmT2